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Classes | |
| class | Euclidean_distance |
| Compute the Euclidean distance between two Points given by a range of coordinates. The points are assumed to have the same dimension. More... | |
| struct | linear_indexing_tag |
| Tag for a linear ordering of simplices. More... | |
| struct | Null_output_iterator |
| class | Off_reader |
| OFF file reader top class visitor. More... | |
| class | Points_3D_off_reader |
| class | Points_3D_off_visitor_reader |
| OFF file visitor implementation according to Off_reader in order to read points from an OFF file. More... | |
| class | Points_off_reader |
| OFF file reader implementation in order to read points from an OFF file. More... | |
| class | Points_off_visitor_reader |
| OFF file visitor implementation according to Off_reader in order to read points from an OFF file. More... | |
| class | Simplex_tree |
| Simplex Tree data structure for representing simplicial complexes. More... | |
| struct | Simplex_tree_options_fast_persistence |
| struct | Simplex_tree_options_full_featured |
Functions | |
| template<typename SimplicialComplexForProximityGraph , typename ForwardPointRange , typename Distance > | |
| Proximity_graph< SimplicialComplexForProximityGraph > | compute_proximity_graph (const ForwardPointRange &points, typename SimplicialComplexForProximityGraph::Filtration_value threshold, Distance distance) |
| Computes the proximity graph of the points. More... | |
| void | read_points (std::string file_name, std::vector< std::vector< double >> &points) |
| Read a set of points to turn it into a vector< vector<double> > by filling points. More... | |
| template<typename Graph_t , typename Filtration_value , typename Vertex_handle > | |
| Graph_t | read_graph (std::string file_name) |
| Read a graph from a file. More... | |
| template<typename Vertex_handle , typename Filtration_value > | |
| bool | read_simplex (std::istream &in_, std::vector< Vertex_handle > &simplex, Filtration_value &fil) |
| Read a face from a file. More... | |
| template<typename Simplex_key , typename Filtration_value > | |
| bool | read_hasse_simplex (std::istream &in_, std::vector< Simplex_key > &boundary, Filtration_value &fil) |
| Read a hasse simplex from a file. More... | |
| template<typename Filtration_value > | |
| std::vector< std::vector< Filtration_value > > | read_lower_triangular_matrix_from_csv_file (const std::string &filename, const char separator= ';') |
| Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole (square) matrix. More... | |
| template<typename OutputIterator > | |
| void | read_persistence_intervals_and_dimension (std::string const &filename, OutputIterator out) |
| std::map< int, std::vector< std::pair< double, double > > > | read_persistence_intervals_grouped_by_dimension (std::string const &filename) |
| std::vector< std::pair< double, double > > | read_persistence_intervals_in_dimension (std::string const &filename, int only_this_dim=-1) |
This file is part of the Gudhi Library. The Gudhi library (Geometric Understanding in Higher Dimensions) is a generic C++ library for computational topology.
Author(s): Pawel Dlotko
Copyright (C) 2016 INRIA (France)
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.
| Proximity_graph<SimplicialComplexForProximityGraph> Gudhi::compute_proximity_graph | ( | const ForwardPointRange & | points, |
| typename SimplicialComplexForProximityGraph::Filtration_value | threshold, | ||
| Distance | distance | ||
| ) |
Computes the proximity graph of the points.
If points contains n elements, the proximity graph is the graph with n vertices, and an edge [u,v] iff the distance function between points u and v is smaller than threshold.
| ForwardPointRange | furnishes .begin() and .end() methods. |
| Distance | furnishes operator()(const Point& p1, const Point& p2), where Point is a point from the ForwardPointRange, and that returns a Filtration_value. |
| Graph_t Gudhi::read_graph | ( | std::string | file_name | ) |
Read a graph from a file.
| Graph_t | Type for the return graph. Must be constructible from iterators on pairs of Vertex_handle |
| Filtration_value | Type for the value of the read filtration |
| Vertex_handle | Type for the value of the read vertices |
File format: 1 simplex per line
Dim1 X11 X12 ... X1d Fil1
Dim2 X21 X22 ... X2d Fil2
etc
The vertices must be labeled from 0 to n-1. Every simplex must appear exactly once. Simplices of dimension more than 1 are ignored.
| bool Gudhi::read_hasse_simplex | ( | std::istream & | in_, |
| std::vector< Simplex_key > & | boundary, | ||
| Filtration_value & | fil | ||
| ) |
Read a hasse simplex from a file.
File format: 1 simplex per line
Dim1 k11 k12 ... k1Dim1 Fil1
Dim2 k21 k22 ... k2Dim2 Fil2
etc
The key of a simplex is its position in the filtration order and also the number of its row in the file. Dimi ki1 ki2 ... kiDimi Fili means that the ith simplex in the filtration has dimension Dimi, filtration value fil1 and simplices with key ki1 ... kiDimi in its boundary.
| std::vector<std::vector<Filtration_value> > Gudhi::read_lower_triangular_matrix_from_csv_file | ( | const std::string & | filename, |
| const char | separator = ';' |
||
| ) |
Read a lower triangular distance matrix from a csv file. We assume that the .csv store the whole (square) matrix.
Square matrix file format:
0;D12;...;D1j
D21;0;...;D2j
...
Dj1;Dj2;...;0
lower matrix file format:
0
D21;
D31;D32;
...
Dj1;Dj2;...;Dj(j-1);
| void Gudhi::read_persistence_intervals_and_dimension | ( | std::string const & | filename, |
| OutputIterator | out | ||
| ) |
Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death The output iterator out is used this way: *out++ = std::make_tuple(dim, birth, death); where dim is an int, birth a double, and death a double. Note: the function does not check that birth <= death.
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inline |
Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death The return value is an std::map<dim, std::vector<std::pair<birth, death>>> where dim is an int, birth a double, and death a double. Note: the function does not check that birth <= death.
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inline |
Reads a file containing persistence intervals. Each line might contain 2, 3 or 4 values: [[field] dimension] birth death If only_this_dim = -1, dimension is ignored and all lines are returned. If only_this_dim is >= 0, only the lines where dimension = only_this_dim (or where dimension is not specified) are returned. The return value is an std::vector<std::pair<birth, death>> where dim is an int, birth a double, and death a double. Note: the function does not check that birth <= death.
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inline |
Read a set of points to turn it into a vector< vector<double> > by filling points.
File format: 1 point per line
X11 X12 ... X1d
X21 X22 ... X2d
etc
| bool Gudhi::read_simplex | ( | std::istream & | in_, |
| std::vector< Vertex_handle > & | simplex, | ||
| Filtration_value & | fil | ||
| ) |
Read a face from a file.
File format: 1 simplex per line
Dim1 X11 X12 ... X1d Fil1
Dim2 X21 X22 ... X2d Fil2
etc
The vertices must be labeled from 0 to n-1. Every simplex must appear exactly once. Simplices of dimension more than 1 are ignored.
| GUDHI Version 2.1.0 - C++ library for Topological Data Analysis (TDA) and Higher Dimensional Geometry Understanding. - Copyright : GPL v3 | Generated on Wed Jan 31 2018 09:40:55 for GUDHI by Doxygen 1.8.11 |